Instructions to use ctheodoris/Geneformer with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use ctheodoris/Geneformer with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("fill-mask", model="ctheodoris/Geneformer")# Load model directly from transformers import AutoTokenizer, AutoModelForMaskedLM tokenizer = AutoTokenizer.from_pretrained("ctheodoris/Geneformer") model = AutoModelForMaskedLM.from_pretrained("ctheodoris/Geneformer") - Inference
- Notebooks
- Google Colab
- Kaggle
allow model_type valid options to take params model_type : {"Pretrained", "GeneClassifier", "CellClassifier", "MTLCellClassifier", "MTLCellClassifier-Quantized"}
#390
by madhavanvenkatesh - opened
geneformer/in_silico_perturber.py
CHANGED
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@@ -60,7 +60,7 @@ class InSilicoPerturber:
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"genes_to_perturb": {"all", list},
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"combos": {0, 1},
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"anchor_gene": {None, str},
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-
"model_type": {"Pretrained", "GeneClassifier", "CellClassifier"},
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| 64 |
"num_classes": {int},
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"emb_mode": {"cls", "cell", "cls_and_gene", "cell_and_gene"},
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"cell_emb_style": {"mean_pool"},
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"genes_to_perturb": {"all", list},
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"combos": {0, 1},
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"anchor_gene": {None, str},
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| 63 |
+
"model_type": {"Pretrained", "GeneClassifier", "CellClassifier", "MTLCellClassifier", "MTLCellClassifier-Quantized"},
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| 64 |
"num_classes": {int},
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| 65 |
"emb_mode": {"cls", "cell", "cls_and_gene", "cell_and_gene"},
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| 66 |
"cell_emb_style": {"mean_pool"},
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